Introduction: Nephrolithiasis is a multifactorial disease related to genetic disorders and environmental factors. Kidney stones are more common in adults and are associated with several metabolic and anatomical disorders. The major anatomical abnormalities, such as obstruction of the ureteropelvic junction, horseshoe kidney, complete or incomplete duplicated ureter, bifid pelvis, and medullary sponge kidney, are known to be responsible for stone formation. The objective of this study is to evaluate anatomical alterations in patients with nephrolithiasis in our region. Methods: Retrospective study on 1,378 patients with evidence of recent formation of kidney stones. Laboratory investigation and chemical analysis were performed when stones were available. Renal imaging techniques comprised at least renal ultrasound and excretory urography. Results: Of the 1,378 patients with nephrolithiasis cared for, only 367 (26.5%) (mean age, 36.8 ± 4.3 years) underwent anatomical investigation, of whom 198 (54.5%) were females. At least one anatomical alteration was found in 132 (36%) patients, the most common being renal cyst, completely or incompletely duplicated ureter, and obstruction of the ureteropelvic junction. Conclusions: Anatomical alterations were found in 36% of the investigated patients. Renal cyst, ureteral duplication, and obstruction of the ureteropelvic junction were the most frequently found anatomical alterations in the group.