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As I've been reading through the lore, it’s been noted that a standard Space Marine stands head and shoulders from a typical human in terms of height (7-8ft).

Size comparison of different characters

While a Primarch possesses an average height of 10-11 ft.

Primarch

Since the Primarchs were direct gene creations from the Emperor I assume his height is also in this range.

Before the Age of Strife, and in known history the Emperor was living among Humanity Influencing it from the shadows. How would he be able to do so when his stature and immense musculature would have set him apart from the populace?

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Besides @Paul's great answer (that there is no proof that Emperor was as tall as Astartes), there is another point to consider:

The Emperor of Mankind is (most likely) the most powerful psyker that ever existed (although eldars who had personal contact with him, called his power "crude"). This means that he can alter the way he is perceived by others. So if he doesn't want to be noticed, then people won't notice him.

  • Actually, great point. This combined with the quotes in @Shade's answer is probably as close to the Answer as we will get without storming the Golden Throneroom. – Paul Sep 13 at 13:45
  • There are a handful appearances of the Emperor in the Horus Heresy series. It seems that the Emperor can appear as how people wants to see him/what He considers the best appearance for a given encounter. IIRC, in the Outcast Dead, he appears as a normal human to the main character. – Taladris Sep 14 at 21:40
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I was not able to find any sources that support your claim that the Emperor was larger than a normal human, and all the lore says that he did spend his mortal days living in secret among normal people (I don't have digital copies of the lore books, but the Lexicanum, while a wiki is pretty faithful to the lore.

We can infer from those canonical assertions and lack of contrary assertions that he simply wasn't outside the normal human range of size. Occam's Razor and all that.

As for why the Astartes were taking from his genes but were huge, remember that they weren't precisely clones. There was a process by which the emperor created them, but it involved more than just a syringe full of Emperor Juice(tm), they added organs, they rebuilt musculature, etc.

Again from the Lexicanum:

the Primarchs were created by the Emperor with the aid of forbidden sciences and arcane lore derived from the Warp

So at best they were genetically engineered beings which had aspects of their makeup influenced by the Emperor, much like you're not a perfect clone of your parents and can potentially be significantly larger or smaller than them, especially once environmental factors come into play. Arguably, there could actually be a lot less of the Emperor's actual genetic code compared to your parents' in the primarchs and one could still claim that his seed was 'used' in their creation, though the Lexicanum says they did start as clones. But clones under the influence of science and Warp-based lore would probably result in significant mutations (further evidenced by some of the traits of the primarchs like angels wings on Sanguinius and similar).

  • However, I've not seen any illustration where he isn't the same height as a Primarch, though his armor's lower legs could be stilts. – Stop Harming Monica Sep 11 at 21:17
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    @OrangeDog You could be onto something. Maybe he's just 2 guys in a tall suit (of power armour). – Kakturus Sep 12 at 9:01
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    He's actually four or five Squats. – delinear Sep 12 at 14:53
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    @delinear Its only three, but they're exceptionally large. – T.J.L. Sep 12 at 16:55
  • Actually, what the Inquisition and HIgh Lords of Terra are hiding, is that this is what happened to the Ork brainboyz. The Emperor is actually 15 hyper intelligent Snotlings. – Paul Sep 13 at 13:42
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There is this one story in the Horus Heresy book Tales of Heresy, The Last Church by Graham McNeill, where the Emperor goes and wants to see the last church. Some quotes:

The Emperor enters church as appearing as a normal man:

A hooded figure was silhouetted in the doorway to the narthex, tall and swathed in a long cloak of scarlet.

...

'No,' said the man, pulling back his hood to reveal a stern, but not unkind face - a remarkably unremarkable face that seemed at odds with his martial bearing.

...

The chair creaked under the weight of his guest...

...

Now that Revelation had sat down, he had removed his scarlet cloak and draped it over the back of his chair. His guest wore utilitarian clothes, identical to those worn by virtually every inhabitant of Terra

The priest describes a vision he had:

'The power of the divine'. Said Uriah. 'I looked up and saw a golden face above me, a face of such radiance and perfection that my tears were no longer shed for pain, but for beauty.

The Emperor then reveals himself:

A golden light built behind Uriah and he saw his shadow thrown out onto the graven surface of the altar. The pearlescent hands of the clock shimmered in the reflected light and the ebony face gleamed.
Where once the church had been gloomy and filled with shadows, it was now a place of light.
Uriah pulled himself to his feet and turned to see a wondrous figure standing before him, towering and magnificent, clad in golden armour fashioned with love and the greatest skill, every plate embossed with thunderbolts and eagles.
Gone was Revelation, and in his place was a towering warrior of exquisite splendour, an exemplar of all that was regal and inspirational in humanity. The armour bulked his form out beyond measure and Uriah felt tears spilling from his eyes as he realised he had seen this breathtakingly, achingly perfect face once before.

So, the emperor appeared to be a normal man, with normal clothes in front of somebody who worships him but does not recognize him just to turn into a fully armoured god emperor (with towering size).

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    Just to add to this answer, there is a mention by John grammatacus in s book (can’t remember which) of how he met the man that would become the emperor of mankind at a dinner event and how he seemed just like a man but could command the room. In addition we have seen throughout the heresy novels that the emperor can appear as different things to different people. – Richard C Sep 15 at 6:53

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