Introduction Roux-en-Y gastric bypass (RYGB) and laparoscopic sleeve gastrectomy (LSG) are the two most frequently performed bariatric operations. These two types of metabolic surgery alter the anatomy and function of digestive tract producing significant weight loss in morbidly obese patients but may lead to malnutrition. Aim Analysis of incidence and severity of malnutrition after bariatric surgery in patients submitted to RYGB or LSG during 12 months of follow-up. Material and Methods Retrospective study of 98 patients after RYGB (n = 47) or LSG (n = 51) assessed for nutritional deficiencies during 12 months after surgery was conducted. The differences in body mass index (BMI) and blood tests including erythrocytes, haemoglobin, total protein, albumin, iron, ferritin, transferrin, vitamin B12, folic acid, calcium and phosphorus concentrations were compared between groups before the operations and at 1 and 12 months. Results Nutritional deficiencies were common before surgery with prevalence up to 19.6% for albumin in the LSG group. Median preoperative BMI levels and albumin concentrations were higher in the RYGB group compared to the LSG group, but there was no difference in percent excess weight loss (%EWL) at 1 and 12 months between LSG and RYGB. One month after LSG erythrocyte count, haemoglobin, iron, ferritin and transferrin levels were significantly higher than in the RYGB group. These differences subsided at 12 months. At 12 months, only the prevalence of vitamin B 12 deficiency was significantly higher in the RYGB group. Conclusion Both RYGB and LSG lead to nutritional deficiencies despite different properties of operations and similar %EWL during follow-up.