ABSTRACT Purpose: To compare the clinical, metabolic, and calculi characteristics of cystine and struvite stone patients after percutaneous nephrolithotripsy (PCNL). Material and Methods: Between January/2006-July/2013, 11 cystine stone patients were treated in our clinic. Of those, 3 were excluded due to incomplete follow-up. Eight cystine stone patients (2 with bilateral disease; 10 renal units-RU) were considered for further analysis. A cohort of 8 struvite stone formers (10RU) was matched having the same age, gender, body mass index (BMI) and Guys stone score. Analyzed parameters comprised demographic data, serum/urinary metabolic evaluation and surgical outcomes. Results: Both groups had 6 female patients. Groups were similar in regards to age, gender, BMI, stone burden, and serum creatinine (p=NS). All patients had PCNL as the first surgical treatment modality. Stone free rate (SFR) after the first PCNL tended to be lower (0%) in the cystine compared to the struvite group (40%)(p=0.08). Final SFR after secondary procedures increased to 70% in cystine and 80% in struvite patients (p=1.0); mean number of procedures to achieve stone free status was higher in the first group (3.57 vs. 2.0;p=0.028). Hypocitraturia was found in all patients, but struvite cases presented with lower mean urinary citrate levels (p=0.016). Other common abnormalities were elevated urinary pH (cystine 75% and struvite 62.5%;p=1.0) and low urinary volume (62.5%,37.5%;p=0.63). Conclusion: Multiple interventions and suboptimal stone free rates are trait of the significant stone burden of struvite and cystine patients. Underlying metabolic abnormalities characterized by increased urinary pH, hypocitraturia and low urinary volume are often encountered in both populations.