Objective To explore the emotional development and nutritional status of HIV/AIDS orphans by their infection status. Methods A community-based cross-sectional survey was conducted during January and December 2005 in four provinces and Bangkok Metropolis where the prevalence of HIV/AIDS among pregnant women was high. The study population consisted of 388 HIV/AIDS orphans who were maternal or paternal or double orphans aged 6–12 years old. The orphans’ main caregivers gave informed consent to the project and assessed the emotional development of their orphaned children. The children were measured for weight, height, and emotional development by standard instruments. They were divided into three groups regarding their HIV/AIDS infection status reported by their caregivers: infected, non-infected, and unknown. The χ2 test was used to determine the association between nutritional status and infection status. Results Regarding HIV/AIDS infected children, 19.1% were infected, 57.5% were not infected, and 23.4% were unknown. The main caregivers of all types of orphans were grandparents. Only 13.7% of infected orphans lived with their mothers. Most caregivers were females and more than 40 years old. Infected orphans had mean scores of overall emotional development and for each domain less than other groups. The mean scores of self-control and quick recovery were significantly different between infected and non-infected groups (P-value < 0.05). Nearly 50% of infected orphans were rather short and approximately 42% were under weight and light. The findings revealed a significant association between height for age, weight for age and infection status of orphans at a P-value of <0.001. Conclusions Orphanhood itself is a vulnerable status and HIV/AIDS infected orphans are most vulnerable. Acceptable and friendly services for orphans and their families are crucial. The services should continue and protect stigmatization.