An unusual alkaloid profile was observed for coca leaf tissue obtained from six field sites in the Putumayo Region of Colombia. A program to control coca leaf production with the aerial spraying of glyphosate on coca fields was known to exist in this area, and local farmers reported that the fields from which the coca leaf tissue came were sprayed aerially. This suggests that the plants in the six fields had been treated with glyphosate before harvest. The alkaloid levels in the leaf tissue from these fields, particularly the reduced production of 3beta-benzoylated tropane alkaloids, such as cocaine, are consistent with the disruption in plant metabolism by a herbicide such as glyphosate. The herbicide alters the shikimic acid pathway. Leaves from treated plants were nearly devoid of cocaine. On the other hand, cocaine levels in leaf tissue from nontreated ECVI and ENVN were 0.53 (plus or minus 0.08 percent) and 0.64 (plus or minus 0.08 percent), respectively. Further analysis showed the presence of several previously undescribed N-nortopane alkaloids, several of which were tentatively identified. These results suggest that applications of glyphosate to coca plants can have dramatic effects on the quantity and quality of alkaloids produced by surviving or subsequent leaves. The description of materials and methods addresses plant material; solvents, chemicals, standards, and materials used in the chemical analysis; the isolation and quantitation of alkaloids; and the gas chromatography-mass spectrometry. 5 figures and 19 references