Hypertrophic pyloric stenosis is a condition in newborns in which the hypertrophic pyloric muscle causes gastric obstructive symptoms of progressive vomiting leading to hypochloremic hypokalemic metabolic alkalosis. The main aim of the research was to assess whether, based on the acid-base status, we can distinguish newborns who vomit due to pylorostenosis, compared with newborns who vomit for other unspecific reasons. The electronic records of patients in the hospital information system treated under the diagnosis Q40.0 (Congenital hypertrophic pyloric stenosis) (n = 69/included in the study = 53) in the period from 1 January 2014 to 1 January 2022 were reviewed retrospectively. For the purposes of the control group, the electronic records of patients treated in the emergency department with a diagnosis of R11.0 (Nausea and vomiting) (n = 53) without an established cause were randomly reviewed. In addition to the main aim, other research outcomes were to determine differences between groups in the following variables: duration of symptoms, family history, birth (preterm, term, post-term), birth weight, weight during examination, difference between birth weight and weight during an examination, type of vomiting, the thickness of the muscle wall and its length, and to calculate whether there is a correlation between the thickness and length of the pylorus muscle and the duration of vomiting in relation to variables from acid-base status. In relation to the variables of interest between the groups, statistically significant differences were observed in the duration of symptoms (Mdn 4 vs. 2 days, p = 0.002), weight at examination (Mean 3880 vs. 4439 g, p = 0.001), difference in weight between birth and examination (Mean 374 vs. 1010 g, p < 0.0001), and type of vomiting (explosive 45 vs. 22, p = 0.023). In the acid-base status between the groups, a statistically significant difference was recorded for pH (Mdn 7.457 vs. 7.422, p < 0.0001), bicarbonate (Mdn 25 vs. 23 mmol/L, p = 0.000), total carbon dioxide (Mdn 25 vs. 24 mmol/L, p = 0.011), base excess (Mdn 0.8 vs. -1.3 mmol/L, p = 0.000), potassium (Mdn 5 vs. 5.3 mmol/L, p = 0.006), ionized calcium (Mdn 1.28 vs. 1.31 mmol/L, p = 0.011), and glucose (Mdn 4.5 vs. 4.9 mmol/L, p = 0.007). Regardless of the group, the correlations between the duration of vomiting (r = 0.316, p = 0.021 vs. r = 0.148, p = 0.290) and the thickness (r = 0.190, p = 0.172) and length (r = 0.142, p = 0.311) of the pylorus muscle in relation to pH did not exist or were weak. In a world where radiological methods are not equally available everywhere, with promising acid-base indicators, prospective multicenter studies and meta-analyses must be pursued in the future in order not to miss the possible much greater diagnostic potential of acid-base status.