To examine the association between beta-globin sequence variations and phenotypes of sickle-cell disease (SCD) complications among Palestinian refugees in Lebanon correlating them with chromatographic readings and co-inheritance with β-thalassemia traits. Methods: This cross-sectional study included 47 Palestinian refugees aged 4 to 54 living in different regions in Lebanon during the year 2015. Participant filled a well-designed questionnaire. Deoxyribonucleic acid (DNA) was purified from the blood collected from all participants, followed by polymerase chain reaction (PCR) amplification of exon 1, exon 2, and IVS 1 of hemoglobin beta. Multiple sequence alignment for comparative analysis was performed against normal hemoglobin sequences. Results: In addition to well-known SCD mutations, rare beta globin variations were identified. Participants with these variations have phenotypic thalassemia despite the absence of known β-thalassemia mutations. Conclusion: The genetic variation seen among our study population is correlated with reduced beta globin transcription, and phenotypic β-thalassemia complications among SCD patients under study.