Periparturient cows go through a period of immune suppression often marked by immune cell dysfunction. Further exacerbation of this dysfunction through earlylactation excessive energy deficit (EED) has been associated with increased susceptibility to infectious conditions such as mastitis. Our objective was to explore the association of milk somatic cell score (SCS) and clinical mastitis (CM) diagnosis in cows identified with EED, diagnosed using each of the following: blood and milk β-hydroxybutyrate (BHB), milk predicted blood nonesterified fatty acid (mpbNEFA) concentrations, or milk de novo fatty acid (FA) relative percentages (rel %). We analyzed data collected from 396 multiparous Holstein cows from 2 New York farms in a prospective cohort study. Coccygeal vessel blood samples and composite milk samples were collected twice weekly from 3 to 18 days in milk (DIM) for a total of 4 time points per cow (T1, T2, T3, T4). Blood was analyzed using a hand-held meter, and milk was analyzed using Fourier-transform mid-infrared spectrometry for milk BHB and mpbNEFA concentrations, milk de novo FA rel %, and somatic cell count. Excessive energy deficit was diagnosed as blood BHB ≥ 1.2 mmol/L, milk BHB ≥ 0.14 mmol/L, mpbNEFA ≥ 0.55 mmol/L, or de novo FA ≤ 22.7 rel %, depending on the model. Clinical mastitis cultures were collected from 4 to 60 DIM by on-farm personnel. Incidence of hyperketonemia as determined by blood BHB was 13.4%, and incidence of CM was 23.9%. Separate repeated-measures ANOVA models were developed for each EED diagnostic analyte for parity groups 2, 3, and ≥4 to assess differences in SCS; t-test analyses were similarly used to assess the association of each diagnostic analyte with CM at each time point. For all diagnostic analytes, apart from milk BHB, cows diagnosed with EED tended to have lower SCS than their non-EED counterparts. This was especially apparent at T1 for all parity groups, and at T2, T3, and T4 for blood BHB and mpbNEFA. For EED diagnosis via mpbNEFA, mean SCS were lower in parity ≥4, with a difference in mean SCS between EED and non-EED animals of 0.7 SCS units, equating to a somatic cell count in EED animals approaching half that of non-EED (EED = 67,000 cells/mL, non-EED = 107,000 cell/mL). No important relationships were observed between CM diagnosis and blood BHB, milk BHB, or mpbNEFA. For de novo FA rel %, reductions in this analyte were noted before CM diagnosis at all time points. Although the relationship between EED and CM is still unclear, our findings suggest that cows in EED, diagnosed using blood BHB or mpbNEFA during the first 18 DIM, have a tendency toward lower SCS compared with their non-EED counterparts.