To identify the underlying subtypes of hidradenitis suppurativa (HS), we performed latent class analysis on prospective clinical data of 618 consecutive patients seen between 2002 and 2010. The median patient age was 31 years (Q1=26; Q3=38), median age at HS onset was 20 years (16-25), and median Sartorius score was 18 (11-19); 34.4% of patients were of Hurley stage II or III. A three-class model showed the best fit. Latent class 1 (LC1) patients (48%) had a high probability of breast and armpit lesions (0.74) and hypertrophic scars (0.41). LC2 patients (26%) had a high probability not only of breast and armpit lesions (0.96) but also of lesions in the ears, chest, back, or legs (0.55); follicular lesions (pilonidal sinus: 0.48; comedones: 0.74); severe acne (0.47); and a family history of HS (0.44). Compared with LC1 patients, LC2 patients were more often male (odds ratio, 4.6; 95% confidence interval, 3-7; P<0.001) and current smokers (2.2; 1.3-3.9; P=0.005), and had greater disease severity (odds ratio, 1.6; 1.3-1.9; P<0.001). LC3 was characterized by gluteal involvement (0.54), papules, and folliculitis (0.71). LC3 patients were less often obese (0.6; 0.3-0.95; P=0.03) and had less severe disease (0.9; 0.7-1.1; P<0.001). These three phenotypes ("axillary-mammary", "follicular", and "gluteal") may help stratify patients for clinical trials.