Lepidium meyenii (Maca) is one of the few plants that can be cultivated in the harsh climate of the Andes. Its nutritious hypocotyl is traditionally used as food and medicine, and Maca products are increasingly becoming popular in the western world as tonics. This paper describes the first analytical method allowing the determination of the main macamides and macaenes, the marker compounds of L. meyenii. A separation within 35 min was possible by using a C-12 stationary phase, an acidic mobile phase comprising of acetonitrile and water, and raising the column temperature to 40 °C. By monitoring the separation at 210 and 280 nm, the markers were detectable as low as 0.40 μg/ml. In order to validate the method, accuracy, precision, linearity, limit of detection and intra/inter day repeatability were determined. The analysis of several commercially available Maca products showed a similar qualitative pattern but significant differences in the quantitative composition. The percentage of total markers in the preparations varied from 0.15 to 0.84%, resulting in daily intakes for the consumer from 1.52 to 14.88 mg, respectively.