The prevalence of non-cigarette tobacco product use is on the rise across the globe, especially for waterpipes (also known as hookah, narghile, and shisha) and electronic cigarettes (e-cigarettes). The scientific literature reveals that waterpipe tobacco smoking is associated with exposure to a variety of toxicants that can cause short- and long-term adverse health events. In contrast, there is far less evidence of health harms related to e-cigarette use, although the variety of products in this category makes it difficult to generalize. We searched the PubMed database for all publications on waterpipes and e-cigarettes from January 2000 to March 2014. The number of publications on waterpipes rose in a slow, linear pattern during this time, while the number of publications on e-cigarettes showed exponential growth. The different trends suggest there may be more interest in studying a novel nicotine product (the e-cigarette) over a traditional tobacco product (the waterpipe). We posit that, although the specific research needs for these products are different, public health would be served best by a more equitable research approach. Scientists should continue to devote attention to understanding the unknown long-term health effects of e-cigarettes and their potential to serve as harm reduction or smoking cessation tools while simultaneously investigating how to reduce waterpipe smoking given that it exposes users to toxicants known to cause harm to health. Recent regulatory action in the United States, which proposes to include waterpipes and e-cigarettes under some of the same regulations as tobacco cigarettes, makes such research particularly timely.