Objective Early diagnosis of pyogenic vertebral osteomyelitis (PVO) is frequently difficult. There are, however, few studies that have investigated the diagnostic performance of PVO in Japan. Our aim was to analyze the diagnostic performance and identify clinical factors associated with the diagnostic delay of PVO. Materials and Methods We performed hospital-based retrospective case analysis. All patients with PVO were identified from the computerized medical database at Okinawa Chubu Hospital in Okinawa, Japan, from January 1985 to December 2004. We collected the following data; baseline information; laboratory tests; clinical and microbiologic outcomes; and diagnostic process. We used multivariable-adjusted linear regression to identify significant factors associated with patient and hospital delay to the diagnosis of PVO. Results We reviewed total of 209,428 patients hospitalized during the 20-year study period. Of those, we identified 51 patients with PVO. Eighty percent of these patients were misdiagnosed at their initial clinical encounters. Median duration from the symptom onset to the diagnosis was 19 days. Median durations of patient factor and hospital factor that contributed to the total delay were 1 and 8 days, respectively. Significant patient factor that contributed to delay was cognitive dysfunction. Conclusions Cognitive dysfunction is a risk factor for patient delay for visiting physicians in patients with PVO. Diagnosis of PVO is difficult at the initial clinical encounter. High index of suspicion is needed for more rapid diagnosis of PVO.