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Introduction East Africa countries (Tanzania, Kenya, and Uganda) are among tuberculosis high burdened countries globally. As we race to accelerate progress towards a world free of tuberculosis by 2035, gaps related to screening and diagnosis in the cascade care need to be addressed. Methods We conducted a three-year (2015–2017) retrospective study using routine program data in 21 health facilities from East Africa. Data abstraction were done at tuberculosis clinics, outpatient departments (OPD), human immunodeficiency virus (HIV) and diabetic clinics, and then complemented with structured interviews with healthcare providers to identify possible gaps related to integration, screening, and diagnosis of tuberculosis. Data were analyzed using STATA™ Version 14.1. Results We extracted information from 49,454 presumptive TB patients who were registered in the 21 facilities between January 2015 and December 2017. A total of 9,565 tuberculosis cases were notified; 46.5% (4,450) were bacteriologically confirmed and 31.5% (3,013) were HIV-infected. Prevalence of tuberculosis among presumptive pulmonary tuberculosis cases was 17.4%. The outcomes observed were as follows: 79.8% (7,646) cured or completed treatment, 6.6% (634) died, 13.3% (1,270) lost to follow-up or undocumented and 0.4% (34) treatment failure. In all countries, tuberculosis screening was largely integrated at OPD and HIV clinics. High patient load, weak laboratory specimen referral system, shortage of trained personnel, and frequent interruption of laboratory supplies were the major cited challenges in screening and diagnosis of tuberculosis. Conclusion Screening and diagnostic activities were frequently affected by scarcity of human and financial resources. Tuberculosis screening was mainly integrated at OPD and HIV clinics, with less emphasis on the other health facility clinics. Closing gaps related to TB case finding and diagnosis in developing countries requires sustainable investment for both human and financial resources and strengthen the integration of TB activities within the health system.