Epidemiologic and animal data indicate that night shift work might increase the risk for breast cancer. We evaluated the association of night work with different clinical types of breast cancer in a population based case-control study (MCC-Spain study) taking into account chronotype, an individual characteristic that may relate to night shift work adaptation. Lifetime occupational history was assessed by face-to-face interviews and shift work information was available for 1708 breast cancer cases and 1778 population controls from 10 Spanish regions, enrolled from 2008 to 2013. We evaluated three shift work domains, including shift work type (permanent vs rotating), lifetime cumulative duration and frequency. We estimated odds ratios (OR) for night work compared to day work using unconditional logistic regression models adjusting for confounders. Having ever worked permanent or rotating night shift was associated with an increased risk for breast cancer compared to day workers [odds ratio (OR) 1.18; 95 % CI 0.97, 1.43]. Chronotype was differentially associated with breast cancer depending on the duration of night shift work. Risk was higher in women with invasive tumors (OR 1.23; 95 % CI 1.00, 1.51) and for estrogen and progestagen positive tumors among premenopausal women (OR 1.44; 95 % CI 1.05, 1.99). Having ever performed night shift was associated with a small increased risk for breast cancer and especially in subgroups of women with particular hormone related characteristics.