Zidovudine injection is used to treat HIV, which causes the acquired immunodeficiency syndrome (AIDS). Zidovudine is also given during pregnancy to prevent an HIV-infected woman from passing the virus to her baby. Zidovudine is not a cure for HIV or AIDS.ess serious side effects may include: 1  sleep problems (insomnia); 2  mild nausea, constipation; 3  joint pain; 4  headache; or. 5  changes in the shape or location of body fat (especially in your arms, legs, face, neck, breasts, and trunk).