Aim: This study aimed to assess the relationship between the three-dimensional (3D) alignment of short tapered-wedge cementless stems and bone mineral density (BMD) changes in patients followed up for 5 years after total hip arthroplasty (THA). Methods: We retrospectively analysed the hips of 52 patients who underwent THA using short tapered-wedge cementless stems at our institution from 2013 to 2016 with complete 5-year follow-up data. We evaluated the relationship between stem alignment, measured using a 3D-templating software, and BMD changes in the 7 Gruen zones. Results: After 1 year, significant negative correlations between varus insertion and a decrease in BMD in zone 7 and between flexed insertion and decreases in BMD in zones 3 and 4 were noted. After 5 years, significant negative correlations between varus insertion and a decrease in BMD in zone 7 and between flexed insertion and decreases in BMD zones 2, 3, and 4 were observed. With increased amounts of varus/flexion stem alignment, the amount of BMD loss decreased. There was no correlation between anteverted stem insertion and changes in BMD levels. Conclusions: Our data showed that stem alignment affects BMD based on 5-year follow-up data after surgery. Careful observation is necessary, especially when using short tapered-wedge cementless stems, as stem alignment may affect changes in BMD levels more than 5 years after surgery.