This study sought to characterize delays and estimate resulting costs during nephrolithiasis surgery. Independent observers documented delays during ureteroscopy (URS) and percutaneous nephrolithotomy (PCNL) procedures. Fifty index cases over a period of three months was considered sufficient to observe the generalizable trends. Operating room staff, excluding the surgeons, were blinded. Time-related metrics and delays preventing case progression were recorded using a smartphone-accessible data-collection instrument. Delays were categorized as: 1) missing equipment; 2) missing personnel; 3) equipment malfunction; or 4) delay due to case complexity. The first two categories were regarded as preventable and the latter two non-preventable. Forty URS and 18 PCNL cases were included. There was a total of 56 delays in 35 (65%) cases. Twelve (67%) PCNLs and 23 (58%) URSs had delays (p=0.57). The mean cumulative delay per case was 3.5±3.2 minutes. Pre-start delays (n=17) were 4.5±3.5 minutes on average while intraoperative delays (n=39) were 3.1±2.9 minutes (p=0.167). Delays were evenly spread among the four categories. Thirty-one (55%) delays were preventable (mean 3.7±3.2 minutes) while 25 (45%) were non-preventable (mean 3.2±3.2 minutes) (p=0.58). This translates to $137 per case in preventable costs. Preventable operative delays are encountered frequently in nephrolithiasis surgery, translating to significant additional charges and costs. We demonstrate a rationale for the development of improved communication and workflow protocols to increase efficiency in endourological surgeries. Key limitations are the observational nature of the study and sample size.