This paper aims to analyze the optimal short term scheduling of hydrothermal systems under pool-bilateral power markets. For that, the short term hydrothermal problem is modified by the inclusion of bilateral power transactions and the split of the vectors of power generations and loads into two components: one traded through the pool and the other traded through bilateral contracts. The transmission losses of each bilateral contract and of the power traded with the pool are also calculated. To allow the allocation of the transactions losses, the modified problem is solved for increments of the system load by a primal-dual interior point optimization algorithm. Results are presented for the Ward-Hale system and a 27-bus equivalent of the Brazilian South Region system.