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In 2021, the US government undertook Operation Allies Welcome, in which evacuees from Afghanistan arrived at 2 US ports of entry in Virginia and Pennsylvania. Because of the rapid evacuation process, the US government granted evacuees an exemption to a Centers for Disease Control and Prevention (CDC) requirement in place at that time—namely, that air passengers present a negative SARS-CoV-2 viral test result or documentation of recovery from COVID-19 before they boarded international flights bound for the United States. This study describes cases of SARS-CoV-2 infection detected among 65 068 evacuees who arrived at the 2 ports of entry in August and September 2021. Because evacuees were a population at increased risk for infection with diseases of public health concern, CDC staff helped coordinate on-site and on-arrival testing, visually observed evacuees for signs and symptoms of communicable disease, and referred evacuees for further evaluation and treatment as needed. CDC staff used antigen or nucleic acid amplification tests at the ports of entry to evaluate evacuees aged ≥2 years without documentation of recent SARS-CoV-2 infection. CDC staff isolated evacuees with confirmed SARS-CoV-2 infection and quarantined their close contacts, consistent with CDC guidance at the time, before evacuees rejoined the repatriation process. Of 65 068 evacuees, 214 (0.3%) were confirmed as having SARS-CoV-2 infection after port-of-entry testing. Cases of measles, varicella, pertussis, tuberculosis, hepatitis A, malaria, leishmaniasis, and diarrheal illness were also identified. Although the percentage of SARS-CoV-2 infection was low in this evacuated population, communicable disease detection at US ports of entry, along with vaccination efforts, was an important part of a multilayered approach to mitigate the transmission of disease in congregate housing facilities and into US communities. [ABSTRACT FROM AUTHOR]