Although uncooperative children with extensive caries can be treated under general anesthesia (GA), they remain at high-risk for caries recurrence. This study aimed to assess the long-term outcome of the dental health of uncooperative healthy children (HC) and special needs patients (SNP) treated under GA at least 2 years before this study. Data were collected via questionnaire and oral examination. Oral hygiene was assessed using the Hygiene Index, while caries were recorded using ICDAS II. The dmfs/DMFS score was calculated for every participant. A total of 69 patients completed the questionnaire, and 37 were clinically examined (HC = 15, SNP = 22). The mean (±SD-standard diviation) follow-up time was 5.5 (±2.55) years, the mean DMFS score for HC was 6.39 (±4.99), and the mean DMFS score for SNP was 12.95 (±12.29). The SNP group had significantly more filled surfaces on permanent teeth than the HC group (6.18 (±6.17) vs. 1.54 (±3.27), p = 0.004). In regard to primary teeth, HC had a higher dmfs, indicating a clear trend for more decayed surfaces in this group of participants (p = 0.08). The DMFS score was significantly higher in children who underwent GA more than 5 years ago. Oral health-related behavior was not improved as expected. Altogether, HC and SNP have poor oral hygiene and high caries risk in primary and permanent dentition, and their treatment remains challenging.