A tropical depression hit the region early on Wednesday, causing flooding, mudslides and lightning strikes in the chain of countries between Mexico and South America. Many areas were cut off as the rain inundated villages and clogged roads.
The destructive weather system that bore down from the Pacific killed 22 in Guatemala, and nine in Honduras, two of whom were struck by lightning, emergency services said.
Hundreds were stranded on the roofs of their homes in Honduras, especially in the southern regions of Choluteca and Valle, local emergency officials said.
In El Salvador, where seven people were killed, President Mauricio Funes declared a state of emergency. At least seven others died and thousands more were evacuated in Nicaragua.
No deaths were reported in Costa Rica, although dozens of families were evacuated from communities on the Pacific coast and the capital, San Jose.
Strong rain continued to fall in parts of Honduras and Guatemala on Saturday, while precipitation was easing in Nicaragua, El Salvador and Costa Rica.
At least four people also died in Mexico earlier in the week when Category 2 Hurricane Jova struck from the Pacific, forcing the country's busiest port to close.
The main cargo port of Manzanillo later reopened.