Micronodular basal cell carcinoma (BCC) may be more difficult to eradicate and prone to recurrence than nodular subtype. The aim of the study was to compare anatomical and histological characteristics of the basal cell carcinomas subtypes and the relationship of the micronodular BCC with other subtypes. Primary BCCs (n = 3074) were classified as superficial, nodular, micronodular, morpheic/infiltrative. The location was head/neck, limbs, chest/abdomen, back or genitals. Fifty-one micronodular BCCs were matched randomly with nodular and infiltrative cases, by age, sex, and tumor site. A modified Clark level was used to classify the tumor depth. Micronodular, nodular and infiltrative BCC were prevalently located in the head/neck (P < 0.0001), while superficial in the other regions (P < 0.0001). The Clark level was comparable between micronodular and infiltrative BCC, while nodular BCC showed a more superficial level than micronodular (P < 0.001) and infiltrative (P < 0.001) BCC. No nodular BCC had level IV and only 37.3% level III, while 92% of both micronodular and infiltrative BCC were level III or IV. The percentage of level IV was 11.8% and 25.5% in micronodular and infiltrative BCC, respectively. In the mid-face/periauricular region, 95.5% of micronodular and 100% of infiltrative cases of were level III or IV, compared to 50% of nodular BCC (P < 0.001). The Clark level of nodular subtype was higher for BCC of mid-face/periauricular than other regions (P < 0.05). It can be concluded that micronodular BCC shows intermediate characteristics compared with nodular and infiltrative subtypes but appears to have a specific individuality making it a distinct subtype.