Genital Herpes: This is often the first consideration for painful genital lesions due to its prevalence and the characteristic presentation of painful vesicles or ulcers. The diagnosis can be confirmed with viral culture, PCR, or serology.

Bartholin's Cyst or Abscess: While not typically described as small lesions, if a Bartholin's gland becomes infected, it can present as a painful, swollen area that might be mistaken for a lesion on the inner labia minora.
Folliculitis: An inflammation of the hair follicles, which can be painful and may resemble small lesions, especially if the follicles become infected.
Genital Warts (Condyloma Acuminata): Though typically not painful, they can cause discomfort and may be mistaken for painful lesions, especially if they become irritated or infected.

Squamous Cell Carcinoma: Although rare, any new, persistent, or changing genital lesion should prompt consideration of malignancy to ensure early detection and treatment.
Syphilitic Chancre: The primary stage of syphilis, which can present as a single, painless (but sometimes painful) ulcer or lesion. Missing this diagnosis can lead to significant morbidity if left untreated.
Lymphogranuloma Venereum (LGV): A sexually transmitted infection caused by certain types of Chlamydia trachomatis, which can cause painful lesions or ulcers, though it more commonly presents with lymphadenopathy.

Molluscum Contagiosum: A viral infection that causes small, pearly, or flesh-colored lesions. While generally not painful, they can become irritated and may be considered in the differential for small genital lesions.
Becker's Nevus: A benign skin growth that can appear as a hyperpigmented lesion and may be considered if the lesion is not typically painful but has an unusual appearance.
Apthous Ulcers: Though more common in the oral cavity, genital apthous ulcers can occur and present as painful lesions, often without an identifiable cause.