The influence of recent and projected changes in atmospheric carbon dioxide concentration [CO2] with and without concurrent increases in air temperature was determined with respect to growth characteristics and production of secondary compounds (alkaloids) in tobacco (Nicotiana tabacum L.) and jimson weed (Datura stramonium L.) over a ca. 50-day period. Rising [CO2] above that present at the beginning of the 20th century resulted in consistent, significant increases in leaf area, and above ground dry weight (both species), but decreased leaf area ratio (LAR) and specific leaf area (SLA) in jimson weed. Increased temperature resulted in earlier development and increased leaf area for both species, but increases in above ground final dry weight were observed only for jimson weed. The secondary compounds evaluated included the alkaloids, nicotine, atropine and scopolamine. These compounds are generally recognized as having impacts with respect to herbivory as well as human physiology. Rising [CO2] reduced the concentration of nicotine in tobacco; but had no effect on atropine, and increased the concentration of scopolamine in jimson weed. However, because of the stimulatory effect of [CO2] on growth, the amount of all three secondary compounds increased on a per plant basis in both species. Temperature per se had no effect on nicotine or scopolamine concentration, but significantly increased the concentration and amounts of atropine per plant. Overall, the underlying mechanism of CO2 induced changes in secondary compounds remains unclear; however, these data suggest that the increase in [CO2] and temperature associated with global climate change may have significant effects not only with respect to herbivory, but on the production of secondary compounds of pharmacological impact.