This paper analyses late presentation (LP) of HIV infection, and its determinants, among men who have sex with men (MSM) in Spain, newly diagnosed with HIV (2003-2011) in 15 sexually transmitted infection/HIV counselling and testing clinics. LP was defined as <350 CD4 cells/µL or AIDS. In total, 3,081 MSM were included (2,499 having CD4/AIDS); overall LP was 25.3%. LP was higher in men older than 34 years, those not previously HIV-tested (adjusted odds ratio (aOR):3.1; 95% confidence intervals (CI):2.3-4.2) , and those tested > 12 months before diagnosis (12-24 months (aOR:1.4; 95% CI:1.0-2.0); > 24 months (aOR:2.2; 95% CI:1.7-3.0)). LP was less likely in MSM reporting a known HIV-infected partner as infection source or symptoms compatible with acute retroviral syndrome. 'Region of birth' interacted with 'educational level' and 'steady partner as infection source': only African and Latin-American MSM with low educational level were more likely to present late; Latin-American men attributing their infection to steady partner, but no other MSM, had LP more frequently. In Spain, HIV testing among MSM should be promoted, especially those > 34 years old and migrants with low educational level. The current recommendation that MSM be tested at least once a year is appropriate.