Salk's inactivated polio vaccine (IPV) was initially favored, but Albert Sabin's oral polio vaccine (OPV), which used a live, attenuated virus, eventually gained prominence due to its ease of administration and potential for long-lasting immunity. This led to a rivalry and debate about the optimal polio vaccination strategy.

The Cutter Incident in 1955 raised concerns about the safety of the Salk vaccine and the quality control measures in vaccine production. This incident led to stricter regulations and improvements in vaccine manufacturing processes.

Salk's efforts to develop an HIV/AIDS vaccine were ultimately unsuccessful, which led to criticism and skepticism from some in the scientific community. However, his work contributed to a better understanding of HIV and potential vaccine strategies.

Salk's high profile and public recognition sometimes drew criticism from colleagues who felt he received disproportionate credit for the collective efforts of his research team.