When to submit?

[hippyscientist]

I know earlier is better. I have 2 excellent LORs but my third is from my MSc supervisor. However, I will not start working with him until the end of September so the earliest he could write a reference would be mid-October (we have a strong email relationship currently). Is this cutting it a bit fine for submission deadlines? One of my school deadlines is 1st November (which seems very early).

[med latte]

Has he already agreed to be a reference? Does he know you outside of your current email relationship? The best references will be people who know you well and can give specific examples to back up the claim that you are an ideal candidate. The writers will be asked how long they have known you.

Is this for a masters or Ph.D. program? 

[hippyscientist]

Sorry, should have said - it's for a PhD application. I agree that I would prefer to have a third reference from my undergrad institution but my applications specifically state a reference from the most recent school attended so he will have to be the reference. Yes, he has agreed to write one for me, and will know me well (personal tutor, research supervisor, work in his lab), just not for very long. However, he should be able to accurately comment on my work and ability to conduct PhD level research. 

[PoliticalOrder]

It doesn't matter when you submit your application as long as it's before the deadline.