In this paper, we analyze the morphology of the Andes of Peru and its evolution based on the geometry of river channels, their bedrock profiles, stream gradient indices and the relation between thrust faults and morphology. The rivers of the Pacific Basin incised Mesozoic sediments of the Marañon thrust belt, Cenozoic volcanics and the granitic rocks of the Coastal Batholith. They are mainly bedrock channels with convex upward shapes and show signs of active ongoing incision. The changes in lithology do not correlate with breaks in slope of the channels (or knick points) such that the high gradient indices (K) with values between 2,000-3,000 and higher than 3,000 suggest that incision is controlled by tectonic activity. Our analysis reveals that many of the ranges of the Western Cordillera were uplifted to the actual elevations where peaks reach to 6,000m above sea level by thrusting along steeply dipping faults. We correlate this uplift with the Quechua Phase of Neogene age documented for the Subandean thrust belt. The rivers of the Amazonas Basin have steep slopes and high gradient indices of 2,000-3,000 and locally more than 3,000 in those segments where the rivers flow over the crystalline basement of the Eastern Cordillera affected by vertical faulting. Gradient indices decrease to 1,000-2,000 within the east-vergent thrust belt of the Subandean Zone. Here a correlation between breaks in river channel slopes and location of thrust faults can be established, suggesting that the young, Quechua Phase thrust faults of the Subandean thrust belt, which involve Neogene sediments, influenced the channel geometry. In the eastern lowlands, these rivers become meandering and flow parallel to anticlines that formed in the hanging wall of Quechua Phase thrust faults, suggesting that the river courses were actively displaced outward into the forelan