Atypical femur fracture (AFF), a serious complication of long-term bisphosphonate therapy, is usually preceded by an incomplete fracture appearing on the lateral femur. AFF is most likely the result of severely suppressed bone turnover (SSBT). However, the differences in bone structure and turnover between patients with incomplete and complete AFF remain unknown. We examined trans-iliac bone biopsies from 12 white postmenopausal women with AFF (incomplete = 5; complete = 7) on BP therapy of >5 years and 43 healthy white premenopausal women. Histomorphometric measurements were performed separately in cancellous, intracortical and endosteal envelopes. Of the 43 histomorphometric measurements on 3 difference bone surfaces (cancellous, intracortical and endosteal), only 2 bone resorption variables (Oc.S/BS and Oc.S/NOS) on the endosteal surface were significantly lower in patients with complete AFF than those with incomplete AFF. Compared to healthy premenopausal women, the trabecular bone volume, thickness and number were all significantly lower in patients with AFF. The dynamic bone formation variables in patients with AFF were significantly reduced on all bone surfaces. The likelihood of a biopsy with no tetracycline labeling was significantly higher in AFF patients than in healthy premenopausal women. Based on these results, we conclude that there are no significant differences in bone turnover between patients with incomplete and complete AFF, suggesting that the suppression of bone turnover had already existed in the femur with incomplete AFF. Compared to healthy premenopausal women, bone turnover is similarly suppressed in patients with either type of AFF.