<b><i>Introduction:</i></b> Genetic biomarkers have the potential to be used in personalised dentistry for improved prevention and decision-making in caries management. The amylase alpha 1 gene (<i>AMY1</i>) encodes salivary α-amylase and may be one such biomarker. We examined the association between <i>AMY1</i> copy number variation (CNV) and dental caries experience in adults. <b><i>Materials and Methods:</i></b> A stratified random sample of 193 participants from the Lithuanian National Oral Health Survey (LNOHS) agreed to provide saliva samples and were included in this analysis (age 35–44 years; participation rate 43%). Information on socio-demographic and behavioural characteristics was taken from the LNHOS, which used the self-administered World Health Organisation (WHO) questionnaire. Data on fluoride levels in drinking water at the recruitment areas was recorded based on information provided by water suppliers. Dental caries experience was recorded at a surface level (smooth-surface and occlusal-surface decayed, missing, filled surfaces [D₃MFS] score) by one trained and calibrated examiner using WHO criteria, and subsequently dichotomised for the statistical analyses. DNA extracted from saliva samples was used to investigate <i>AMY1</i> CNV using the QX200 droplet digital PCR system. Bivariate and multivariable statistical analyses were employed. <b><i>Results:</i></b> When compared to participants with an <i>AMY1</i> copy number (CN) of 2–3, higher odds of smooth-surface D₃MFS &#x3e;14 was observed for participants with a CN of 4–5 (OR 13.3, 95% CI 2.1–86.3), 6–9 (OR 7.0, 95% CI 1.4–34.1), and 10–16 (OR 5.8, 95% CI 1.2–32.2). Female sex was independently associated with a smooth-surface D₃MFS &#x3e;14 (OR 5.7, 95% CI 1.9–17.2). <b><i>Conclusions:</i></b> Our study demonstrated an association between <i>AMY1</i> CNV and high smooth-surface caries experience. Studies with larger sample sizes are needed to validate this association.