Background Sildenafil is a cyclic guanosine monophosphate-specific phosphodiesterase-5 inhibitor used for treating pulmonary hypertension. Although the use of sildenafil in patients under 18 years old is off-label, this inhibitor has been widely prescribed for children treatment at hospitals in Brazil. In this work we evaluated the current practices in using sildenafil in the three main reference hospitals of Rio de Janeiro to design a clinical trial. Then we analyzed the content of sildenafil in powder paper preparations used in these institutions. Methods and Results We assessed the data about the use of sildenafil in three reference hospitals including Instituto Nacional de Cardiologia – INC, Instituto Estadual de Cardiologia Aloysio de Castro – IECAC and Hospital Pro-Cardíaco – HPC. The pharmacy records were analyzed from April 1st, 2008 to April 30th, 2008 and interviews with the pharmacists were also performed. Our results showed that INC used the greatest amount of sildenafil in: treatment of pulmonary arterial hypertension (PAH), management of transient PAH during surgery, preparation for cardiac transplantation and haemodynamic studies during cardiac catheterization. Meanwhile IECAC and HPC used sildenafil only for treating PAH in few patients during the period evaluated. In INC and IECAC, sildenafil was available in tablets, and powder papers prepared by two private pharmacies and one public hospital pharmacy. In contrast all patients of HPC received sildenafil in tablets with no external manipulation. Our quantification analysis results using reverse-phase high performance liquid chromatography method showed that powder papers prepared by the private pharmacies from the sildenafil tablets presented only 58.5 to 89.3% of the declared concentration in contrast to samples from the public hospital pharmacy (104.4 to 105.3%). Conclusion Few patients received the prescribed sildenafil dose at the reference hospitals evaluated in Rio de Janeiro, which may importantly compromise this inhibitor effect in the current treatment. This study reinforced the need of checking the practices of preparing and administering sildenafil continually.