The difficulty of early diagnostics of weakly symptomatic clinical course of chronic pyelonephritis (CP) is attributable to the lack of adequate methods. We used a novel Litos system diagnostic technology based on morphological analysis of dehydrated biological fluid The aim of the study was to develop methods for CP diagnostics from morphological characteristics of urine at different stages of the disease. It included 108 patients aged 58+/-1.3 yr with CP and 24 practically healthy subjects. Standard examination of all patients was supplemented by the analysis of urine using the Litos system. It was shown that morphological picture of urine makes it possible to objectively detect not only complete remission or exacerbation of the disease but also partial remission and high risk of CH even in patients with weakly symptomatic clinical course of this pathology. In case of incomplete remission, the treatment requires adequate long-term (three-course) antibacterial therapy despite normal results of urine analysis and microbiological studies. Patients at high risk of CP need to be prescribed preventive phytotherapy.