His mother was very insistent about the importance of education and ensured that he attended Hawarden Grammar School where he won a scholarship and exhibition to study physics at Liverpool University.
He graduated with First Class Honours in 1930 and stayed on to do research at Liverpool into crystal structures using x-ray diffraction.
In Teddington in 1937 he married Jenny Rosenthal (23 January 1910 – 2009) In practical terms, Lipson was in charge of the crystallography group in Cambridge, and took on a key role in nurturing young scientists.
Whilst at the Cavendish he became convinced by contact with P. P. Ewald of the importance of the Fourier transform in X-ray crystallography.
The position carried no title or status, but under his direction it quickly became a world centre for crystallographic research pioneering optical approaches to x-ray diffraction based on the Fourier transform.