Sleeve gastrectomy (SG) is associated with short-term nutritional deficiencies postoperatively. This study evaluates the long-term percent excess weight loss (%EWL), and nutritional deficiencies in a single-center cohort undergoing SG as a primary procedure, with a 6-year follow-up. From January 2005 to December 2010, records of 209 patients who underwent laparoscopic SG were retrieved from a computer database for analysis. 60 out of 209 completed follow-ups of 6 years. Median %EWL at 1, 2, 3, 4, 5 and 6 year postoperatively was 80.9%, 79.1%, 73.8%, 71.8%, 71.5%, and 64.9%, respectively. Prior to surgery, 17.2% had anemia. Deficiencies of iron, ferritin, folic acid, vitamin B12, magnesium, and phosphorus were 22%, 5.3%, 1.4%, 3.8%, 29.7%, 5.3%, respectively. Six years post-surgery, deficiencies of hemoglobin, ferritin, and B12 worsened (36.7%, 43.3%, and 11.7%, p = 0.001, p < 0.001, p = 0.019, respectively), whereas there was no significant difference in deficiencies of iron, folic acid, magnesium, and phosphorus (25%, 1.7%, 20%, and 3%, p = 0.625, p = 0.896, p = 0.139, p = 0.539, respectively). There was elevated PTH before and six years post-surgery (2.9% and 1.7%, p = 0.606). This retrospective study shows that LSG had a considerable effect on specific nutritional deficiencies in our patients at six-year post-surgery.