Introduction Safety in Transfusion Medicine is subject to regulations and government legislation within a total quality framework. The aim of this study was to evaluate the impact of seroprevalence and indeterminate results on lost units and cost per donation. Methods A prospective cross-sectional study was performed in the Blood Bank and Transfusion Therapy Department of the Hospital Central de la Policia Nacional del Perú in Lima, Peru. All completed donations (replacement/voluntary) without complications were included in this study. Every donation met the institutional requirements and quality criteria of Programa Nacional de Hemoterapia y Bancos de Sangre (PRONAHEBAS). Data analysis was achieved using the Statistical Package for the Social Sciences. Results A total of 7723 donations were evaluated during 2014 and 2015 with 493 being seropositive (overall prevalence 5.25%) and 502 having indeterminate results (overall prevalence 5.35%). Thus total loss was 995 units, 437.8 L of blood and 49,750 US dollars. The most common seropositive infectious markers were the core antibody of hepatitis B virus (2.82%) and syphilis (1.02%), and the most common indeterminate results were Chagas disease (1.27%) and the core antibody of hepatitis B virus (1.26%). There was no significant change in the prevalence of seropositivity (p-value = 0.243) or indeterminate results (p-value = 0.227) over the two-year period of the study. A statistical correlation was found between the cost per lost donation and the most prevalent markers (rho = 0.848; p-value = <0.001). Conclusion Seroprevalence was lower than the regional mean, but the prevalence of indeterminate results was elevated causing a great impact on blood supply and economic losses to this institution.