BACKGROUND Tsetse flies (Glossina spp.) are responsible for the transmission of trypanosomes, agents of animal and Human African Trypanosomiasis (HAT). These diseases are associated with considerable animal and human economical loss, morbidity and mortality. The correct identification of trypanosomes species infecting tsetse flies is crucial for adequate control measures. Identification presently requires technically difficult, cumbersome and expensive on-site fly dissection. To obviate this difficulty we explored the possibility of correctly identifying trypanosomes in tsetse collected, under field conditions, only for number determination. METHODOLOGY Tsetse flies, that remained exposed for weeks in field traps in the Vista Alegre HAT focus in Angola, were obtained. The flies were not dissected on site and were stored at room temperature for months. DNA extraction using the whole tsetse bodies and PCR analysis were performed in 73 randomly chosen flies. RESULTS Despite the extensive degradation of the tsetse, DNA extraction was conducted successfully in 62 out of the 73 flies. PCR analysis detected the presence of T. brucei s.l DNA in 3.2 % of the tsetse. CONCLUSIONS This approach could be cost-effective and suitable for vector related HAT control activities in the context of countries where entomological trained personnel is missing and financial resources are limited.