We present 51 heat flow measurements and two geophysical profiles across the West Philippine and Parece Vela basins. We show that both regions have a variable heat flow but that the scatter decreases markedly if we accept as reliable only measurements in areas of uniform sediment drape. Extending this argument to the deep ocean floor shows that the heat flow in these two marginal basins is not necessarily higher than that for deep ocean floor of the same age. On the other hand, the mean depth of both basins is greater and the oceanic crust thinner than the depth and crust of ocean floor of the same age. In the absence of a significant free air gravity anomaly over both basins, we suggest that the thinner crust may account for most of the increase in depth of the two basins. However, more refraction studies are needed to substantiate this difference before this explanation can be unreservedly accepted.