In patients who underwent arthroscopic meniscectomy for medial meniscus tears, the authors wished to ascertain (1) whether varus alignment in the lower extremity would increase after an operation and (2) if so, what the related factors would be. Among 181 patients from 20 to 60 years of age who underwent arthroscopic medial meniscectomy for medial meniscus tears between 2002 and 2005, 56 patients followed for a minimum period of 5 years were enroled for this study. Alignment in the lower extremity was measured preoperatively and again at the last follow-up. Change in varus alignment (the difference between preoperative alignment and alignment at the last follow-up) was analyzed in relation to sex, age, body mass index (BMI), resection amount (partial vs. total), preoperative alignment, and follow-up duration, using multiple linear regression analysis. Varus deformity increased by 1.7° ± 1.5° from a preoperative mean of 2.4° ± 2.4° to a mean of 4.1° ± 3.0° at the last follow-up, which was statistically significant (p = 0.000). From multiple linear regression analysis, only the resection amount (partial meniscectomy or total meniscectomy) was found to be significantly related to the change in varus alignment (p = 0.002). Other factors including sex, age, BMI, preoperative alignment, presence of cartilage injury and follow-up duration were not significantly related to the change in varus alignment after the operation. Arthroscopic meniscectomy performed in patients with medial meniscus tears aggravated varus alignment in the lower extremity at the last follow-up. In addition, the increase in varus deformity was significantly higher among patients with total meniscectomy than among those with partial meniscectomy. Retrospective comparative study, level III.