Abstract Background and Aims The general significance of Balkan endemic nephropathy (BEN) is the association with upper tract urtohelial cancer (UTUC). In published papers studying these two entities, there is large difference between the obtained results. By UTUC research, obtained results are the most diverse in relation to the period and region of research. The aim of the research is to show the discrepancy between the results of the research of UTUC of Jablanica district in relation to the observation period and the type of settlement. Method The research period lasted from 1978-2017. During the analysis of the frequency of UTUC, we used the operative material of Urology Department, Health Care Center, Leskovac , and Urology Clinic, Clinical Center, Nis, Clinical Center, Nis. For practical reasons, this period was devided into two periods, the first (1978-1997) and the second (1998-2017). In order to make classification of settlements we used the data of the Institute of Nephrology and Hemodialysis in Nis (A-endemic regions, B-hypo-endemic, C-non-endemic urban, D-non-endemic rural regions). Data on the total number of Jablanica region population were obtained on the basis of the censuses from 1991 and 2011. The average annual incidence rate (AAIR) was calculated per 100 000 people. Finally, we jointly observed groups A and B (endemic areas) C and D (non-endemic areas) for UTUC. Results The average annual incidence rate (AAIR) in the period of 1978-2017 in endemic settlements of Jablanica region was (11.82), while in hypo-endemic was (4.49) and non-endemic (0.83). The data demonstrated that inhabitants of endemic settlements has 14.24 times higher UTUC frequency in comparison to non-endemic settlements in time span of research. Our research in Jablanica region also demonstrated unexpectedly high frequency of on UTUC not only in endemic settlements with BEN (Kutles village- 1 tumor per 99.63 and AAIR 40.15), but also in some of the non-endemic area (Brejanovac village-1 tumour per 98.75 people and AAIR of 40.50; Rudare village-1 tumour per 139.50 people and AAIR of 28.67; Bogojevce village-1 tumour per 187.63 people and AAIR 21.32). This occurrence of UTUC frequency in some non-endemic settlements refers to the first observed period until no occurrence was recorded in the second observed period. There is a higher UTUC frequency in endemic settlements of 11.37 in the first period (A- AAIR 21.95), while in hypo-endemic (B-AAIR 11.82) is 3.64 higher incedence. In non-endemic settlements (C,D-AAIR 1.09) there is 1.63 higher incidence in comparison to the second period. Observing the periods, there is a higher UTUC frequency of five times in endemic settlements (A, B) of Jablanica region in the first period comparing to the second. The linear trend of UTUC in the 40-year period demonstrates a slow decrease (y= -0.0797x + 4.2846; r2 = 0.2028) in Jablanica region. In the same observed period, linear trend of BEN is in corelation of decreased linear trend of UTUC (y= -0.164x+6.0669; r2 =0.748). Conclusion A forty-year study of UTUC in the Jablanica region showed a discrepancy between the results in relation to the observation period and the type of settlement, which coincides with the generally accepted view that epidemiology is the most fascinating part of BEN. In endemic settlements, in the second observed period, the frequency of UTUC was registered five times lower than in the first, which coincides with the decrease in the frequency of BEN in these settlements.