This study was conducted to determine the composition of staghorn stones and to assess the proportion of infected stones as well as the correlation between infection in the stones and bacteria grown in urine. Samples of 45 consecutive stones removed through anatrophic nephrolithotomic procedures were taken from the operation site and samples of urine were obtained by simultaneous bladder catheterization. The frequency of infection in the stones and correlation between infection of stone and urine samples were determined with respect to the composition of the stones. Twenty-two males and 23 females, with respective mean ages of 48.3 ± 15.6 years and 51 ± 7.4 years, were studied. The stone and urine cultures yielded positive results in ten and 16 patients, respectively, of a total of 45 patients (22.2% and 35.5%, respectively). Calcium oxalate was the main constituent of staghorn stones, seen in 31 patients (68.8%), uric acid in 12 patients (26.6%) and struvite and/or calcium phosphate in 11 patients (24.4%). In seven of ten stones with bacterial growth, bacteria were isolated from urine cultures as well, which accounted for a concordance rate of 70%. The bacteria grown in the stone were the cause of urinary tract infection (UTI) in 43.5% of the cases. Stone infection was significantly associated with UTI (OR = 6.47; 95% CI 1.43-31.7, P = 0.021) and presence of phosphate in the stones (OR = 18, 95% CI 3.28-99.6, P = 0.0006). E. coli was the most common bacteria grown from the stones, and was isolated in 50% of the cases; Ureaplasma urealyticum was the most common organism causing UTI, grown in 62.5% of the urine samples. There was a high concordance rate between bacteria in the stones and urine. These findings indicate that the urine culture can provide information for selection of an appropriate anti-microbial agent for stone sterilization. In addition, preventing re-growth or recurrence of stones and treatment of post-surgical infections would be facilitated based on the results of the urine culture.