The list of number-one singles of 1999 in Italy includes all the songs that reached the top spot on the weekly chart compiled by the Federazione Industria Musicale Italiana (FIMI).
| Week | Single | Artist(s) | Ref. |
|---|---|---|---|
| 1 | "Believe" | Cher | [1] |
| 2 | [2] | ||
| 3 | [3] | ||
| 4 | [4] | ||
| 5 | [5] | ||
| 6 | "Pretty Fly (For a White Guy)" | The Offspring | [6] |
| 7 | [7] | ||
| 8 | [8] | ||
| 9 | [9] | ||
| 10 | "Oggi sono io" | Alex Britti | [10] |
| 11 | "...Baby One More Time" | Britney Spears | [11] |
| 12 | "Snow on the Sahara" | Anggun | [12] |
| 13 | "...Baby One More Time" | Britney Spears | [13] |
| 14 | [14] | ||
| 15 | "Flat Beat" | Mr. Oizo | [15] |
| 16 | "Snow on the Sahara" | Anggun | [16] |
| 17 | "Per te" | Jovanotti | [17] |
| 18 | "I Want It That Way" | Backstreet Boys | [18] |
| 19 | [19] | ||
| 20 | [20] | ||
| 21 | [21] | ||
| 22 | [22] | ||
| 23 | "Beautiful Stranger" | Madonna | [23] |
| 24 | "Unforgivable Sinner" | Lene Marlin | [24] |
| 25 | "Il mio nome è mai più" | Liga-Jova-Pelù | [25] |
| 26 | [26] | ||
| 27 | [27] | ||
| 28 | [28] | ||
| 29 | [29] | ||
| 30 | [30] | ||
| 31 | [31] | ||
| 32 | [32] | ||
| 33 | [33] | ||
| 34 | [34] | ||
| 35 | [35] | ||
| 36 | [36] | ||
| 37 | [37] | ||
| 38 | [38] | ||
| 39 | [39] | ||
| 40 | [40] | ||
| 41 | "New Day" | Wyclef Jean featuring Bono | [41] |
| 42 | "Il mio nome è mai più" | Liga-Jova-Pelù | [42] |
| 43 | "50 special" | Lùnapop | [43] |
| 44 | [44] | ||
| 45 | "Keep On Movin'" | Five | [45] |
| 46 | "La fine del millennio" | Vasco Rossi | [46] |
| 47 | [47] | ||
| 48 | [48] | ||
| 49 | [49] | ||
| 50 | [50] | ||
| 51 | [51] | ||
| 52 | [52] | ||